Problems with the input (from TPM) - How to remove isoforms in WGCNA
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Ortega-C ▴ 10
Last seen 3 months ago

Hello everyone,

I have the TMP from RNAseq data. These data come from Arabidopsis seeds infected with a fungal inoculum. Sequencing reads were aligned to the Arabidopsis transcriptome using Salmon, version 0.14.1 and I get isoforms separately.

My code WGCNA work very well, However, I suspect that there is a problem that I need to solve and I don't know how to do it.

datExpr <- read.csv("TPM_Zscore_Ready.csv", header=TRUE, sep=',') colnames(datExpr) row.names(datExpr) = datExpr$Genes datExpr$Genes = NULL datExpr = dim(datExpr)

my data (imput) looks like this ()with isoforms) Genes AT1G04990.6 AT5G08450.2 AT5G07970.1 AT1G76970.1 AT5G17510.2 AT5G08335.1 AT1G08800.2 AT2G46800.5 AT1G05090.1 AT5G65510.4 AT2G15530.7 AT1G30000.1 AT2G32660.2 AT3G46920.2 AT3G07790.1 AT3G24870.1 AT3G10490.2

So, I don't know how to properly remove isoforms for to have unique genes.

networks on cytoescape and genes selected look as isoforms. I really appreciate if someone can guide me towards the correction.

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Thank you very much

Arabidopsis_thaliana removeisoforms WGCNA • 480 views

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